[2024-01-24 11:22:49,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference
[2024-01-24 11:22:50,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,458] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg59b4392a-0fae-45e3-b2fc-7b8b9a4b982f/GCF_016862975.1_ASM1686297v1_genomic.fna.gz | prodigal -d GCF_016862975.1_ASM1686297v1_genomic.fna/cds.fna -a GCF_016862975.1_ASM1686297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:21,560] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:21,561] [INFO] Task started: HMMsearch
[2024-01-24 11:23:21,561] [INFO] Running command: hmmsearch --tblout GCF_016862975.1_ASM1686297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/reference_markers.hmm GCF_016862975.1_ASM1686297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:21,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:21,964] [INFO] Found 6/6 markers.
[2024-01-24 11:23:22,045] [INFO] Query marker FASTA was written to GCF_016862975.1_ASM1686297v1_genomic.fna/markers.fasta
[2024-01-24 11:23:22,046] [INFO] Task started: Blastn
[2024-01-24 11:23:22,046] [INFO] Running command: blastn -query GCF_016862975.1_ASM1686297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/reference_markers.fasta -out GCF_016862975.1_ASM1686297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:23,181] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:23,185] [INFO] Selected 27 target genomes.
[2024-01-24 11:23:23,185] [INFO] Target genome list was writen to GCF_016862975.1_ASM1686297v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:23,698] [INFO] Task started: fastANI
[2024-01-24 11:23:23,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b4392a-0fae-45e3-b2fc-7b8b9a4b982f/GCF_016862975.1_ASM1686297v1_genomic.fna.gz --refList GCF_016862975.1_ASM1686297v1_genomic.fna/target_genomes.txt --output GCF_016862975.1_ASM1686297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:24:08,219] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:08,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:24:08,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:24:08,248] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:24:08,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:24:08,248] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	100.0	3599	3607	95	conclusive
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	78.5809	764	3607	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.4314	782	3607	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	78.3242	1017	3607	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	78.3225	1001	3607	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.3048	891	3607	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	78.2123	997	3607	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	78.165	833	3607	95	below_threshold
Micromonospora globbae	strain=WPS1-2	GCA_003610785.1	1894969	1894969	type	True	78.061	982	3607	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	78.0305	850	3607	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	78.0121	1040	3607	95	below_threshold
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	78.0027	980	3607	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	77.9959	1061	3607	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	77.8871	875	3607	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	77.843	867	3607	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	77.7889	1197	3607	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	77.5441	1035	3607	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	77.5233	647	3607	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	77.4805	1158	3607	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	77.4707	1043	3607	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	77.3932	1033	3607	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	77.3872	1012	3607	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	77.3423	1041	3607	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	77.3034	1184	3607	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	77.2389	1282	3607	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	77.1861	1235	3607	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	77.0989	988	3607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:24:08,250] [INFO] DFAST Taxonomy check result was written to GCF_016862975.1_ASM1686297v1_genomic.fna/tc_result.tsv
[2024-01-24 11:24:08,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:24:08,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:24:08,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/checkm_data
[2024-01-24 11:24:08,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:24:08,353] [INFO] Task started: CheckM
[2024-01-24 11:24:08,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862975.1_ASM1686297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862975.1_ASM1686297v1_genomic.fna/checkm_input GCF_016862975.1_ASM1686297v1_genomic.fna/checkm_result
[2024-01-24 11:25:50,802] [INFO] Task succeeded: CheckM
[2024-01-24 11:25:50,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:25:50,828] [INFO] ===== Completeness check finished =====
[2024-01-24 11:25:50,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:25:50,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862975.1_ASM1686297v1_genomic.fna/markers.fasta)
[2024-01-24 11:25:50,829] [INFO] Task started: Blastn
[2024-01-24 11:25:50,830] [INFO] Running command: blastn -query GCF_016862975.1_ASM1686297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg982ec2f2-2ff5-49cb-bb7e-134de9a84c34/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862975.1_ASM1686297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:25:52,525] [INFO] Task succeeded: Blastn
[2024-01-24 11:25:52,529] [INFO] Selected 23 target genomes.
[2024-01-24 11:25:52,530] [INFO] Target genome list was writen to GCF_016862975.1_ASM1686297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:25:53,044] [INFO] Task started: fastANI
[2024-01-24 11:25:53,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b4392a-0fae-45e3-b2fc-7b8b9a4b982f/GCF_016862975.1_ASM1686297v1_genomic.fna.gz --refList GCF_016862975.1_ASM1686297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862975.1_ASM1686297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:33,143] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:33,163] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:33,164] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_016862975.1	s__Rugosimonospora africana	100.0	3599	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005885555.1	s__Rugosimonospora sp005885555	79.1142	1059	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	78.4931	780	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	78.3587	934	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	78.3388	998	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	78.3274	1018	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900091605.1	s__Micromonospora tulbaghiae	78.2151	997	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_008119785.1	s__Micromonospora sp008119785	78.1576	1110	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	78.1459	991	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	78.1451	837	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	78.0836	1079	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626635.1	s__Micromonospora musae	78.0268	974	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.26	97.34	0.95	0.93	3	-
GCF_016862915.1	s__Plantactinospora endophytica	77.9212	1149	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091615.1	s__Micromonospora yangpuensis	77.8659	877	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015690345.1	s__Plantactinospora sp015690345	77.7981	937	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	77.7793	1198	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862935.1	s__Plantactinospora mayteni	77.7722	1134	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	77.6502	1051	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751085.1	s__Micromonospora_E sp003751085	77.542	945	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764565.1	s__Phytohabitans suffuscus	77.4674	1163	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764545.1	s__Phytohabitans flavus	77.463	1046	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	77.2002	1230	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	77.1799	986	3607	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:33,165] [INFO] GTDB search result was written to GCF_016862975.1_ASM1686297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:33,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:33,171] [INFO] DFAST_QC result json was written to GCF_016862975.1_ASM1686297v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:33,171] [INFO] DFAST_QC completed!
[2024-01-24 11:26:33,171] [INFO] Total running time: 0h3m44s